This is interesting - I have a similar problem with my girlfriends 01/01/2007 Cooper Auto. I have been worried that it is the chain tensioner problem that affects lots of the MCS
's but after listening to what they sound like on youtube - it is quite a different rattle / chatter that only occurs at a certain temp when the car is under load / in gear at around 2000rpm. It goes once warmed up. We have only owned the car since late August this year and have noticed that it only does it when the engine is cold, particularly on cold mornings. The car has only done 14,000 miles with full Mini TLC history.
I spoke to North Oxford Mini who are local-ish to us and they said on the phone that it could be oil starvation to the tensioner (apparently does affect Coopers as well as Cooper S's) - which could be a simple fix as there is a modified part now - but it could also be more serious if there is wear to the chain resulting in a much more expensive solution - est £7-800.
To me it sounds like a thin metal heat shield panel rattling on the exhaust or something - but I think it's worth getting investigated as in time the risk says it could be pretty expensive if I'm wrong!